A case is described of late-onset glycogenosis type II presenting with an isolated rise in serum transaminase levels. Histological, histochemical, ultrastructural and biochemical examinations performed on muscle biopsy showed the typical laboratory features of late-onset glycogenosis type II, which was diagnosed more than four years before the first appearance of disease-related signs and symptoms. A heterozygote status for the same defect was also demonstrated by enzyme assays in both parents, thus confirming the autosomal recessive mode of inheritance of the disorder. Even though an elevation in transaminases and other serum enzymes of possible muscle origin has been previously described as a diagnostic clue in some unsuspected muscular diseases in childhood, as far as we know no other patient with a sporadic form of glycogenosis type II has been identified when still completely asymptomatic. The possibility of silent primary metabolic diseases and myopathies should be carefully considered when evaluating children with persistently elevated serum transaminases, even in the absence of suggestive anamnestic, familial and physical findings, in order to obtain an early diagnosis and to provide an appropriate genetic counselling.